Bereau Tristan, Walter Luis J, Rudzinski Joseph F
Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany.
Physics Department and CSMB Adlershof, Humboldt-Universitt zu Berlin, 12489 Berlin, Germany.
J Chem Inf Model. 2024 Dec 23;64(24):9413-9423. doi: 10.1021/acs.jcim.4c01754. Epub 2024 Dec 2.
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an acyclic directed graph, providing the entire history of a simulation─from system preparation to property calculations. Martignac connects to NOMAD, such that all simulation data generated are automatically normalized and stored according to the FAIR principles. We present several prototypical Martini workflows, including system generation of simple liquids and bilayers, as well as free-energy calculations for solute solvation in homogeneous liquids and drug permeation in lipid bilayers. By connecting to the NOMAD database to automatically pull existing simulations and push any new simulation generated, Martignac contributes to improving the sustainability and reproducibility of molecular simulations.
尽管分子动力学（MD）模拟应用广泛且影响深远，但却缺乏可追溯性和可重复性。我们引入了Martignac：用于粗粒度（CG）Martini力场的计算工作流程。Martignac将Martini CG MD模拟描述为一个无环有向图，提供了模拟的整个历史记录——从系统准备到属性计算。Martignac连接到NOMAD，以便根据FAIR原则自动对生成的所有模拟数据进行标准化和存储。我们展示了几个典型的Martini工作流程，包括简单液体和双层膜的系统生成，以及溶质在均匀液体中的溶剂化自由能计算和药物在脂质双层膜中的渗透自由能计算。通过连接到NOMAD数据库以自动提取现有模拟并推送生成的任何新模拟，Martignac有助于提高分子模拟的可持续性和可重复性。
